Hi Yang,
In order to figure this out far more information is required:
1) How did you configure the compilation (i.e. what arguments did you pass
to your configure script)?
2) What compilers are you using and what version?
3) If you are running in parallel, what MPI implementation are you using and
what version?
4) What does your run script look like (specifically how are you invoking
sander)?
5) If you are running in parallel, have you tried running on only 1 CPU?
6) Which test case did you try to run that did not pass?
7) When you are running the job does it take up CPU time?
-Dan
On Mon, Mar 29, 2010 at 9:40 PM, Yang Li <chlorin316.hotmail.com> wrote:
>
> Hi,
> I took Dr. Case's recommendation and run a 10 step simulation. The test
> case did not pass, it was running and I tried to tail -f the .out file, but
> nothing showed up. The simulation ran for the entire weekend and there's no
> output file so I stopped it.
> What do you think the problem is?
>
>
> With regards,
> Yang
>
> > From: carlos.simmerling.gmail.com
> > Date: Mon, 29 Mar 2010 15:58:40 -0400
> > Subject: Re: [AMBER] simulation under pressure
> > To: amber.ambermd.org
> >
> > have the test cases passed? is the job still getting CPU time? do you get
> > any output at all?
> >
> > On Mon, Mar 29, 2010 at 3:53 PM, Yang Li <chlorin316.hotmail.com> wrote:
> >
> > >
> > > Hi, Dr. Case,
> > >
> > > Thank you for you recommendations. I checked and my prmtop was
> > > periodic and solvated. I tried to run a 10 step simulation, here is my
> > > input file.
> > >
> > > DNA 12-ATmer simulation under 100atm
> > > &cntrl
> > > imin = 0, irest = 1,
> > > igb = 0, ntx = 5,
> > > ntt = 3, gamma_ln = 1.0,
> > > tempi = 300.0, temp0 = 300.0
> > > ntp = 1, taup = 2.0, pres0 = 100,
> > > ntb = 2, ntc = 2, ntf =2,
> > > nstlim = 10, dt = 0.01
> > > ntwx = 1, ntpr =1
> > > cut = 12.0
> > > /
> > >
> > >
> > > However, the simulation has run for the entire weekend again and did
> > > not finish on the 3G processor.
> > >
> > > Please let me know what I can do.
> > >
> > >
> > > With regards,
> > >
> > > Yang
> > > _________________________________________________________________
> > > Check your Hotmail from your phone.
> > >
> > >
> http://go.microsoft.com/?linkid=9712957_______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _________________________________________________________________
> Check your Hotmail from your phone.
>
> http://go.microsoft.com/?linkid=9712957_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 29 2010 - 19:30:04 PDT
